Man pages for Struglab/RVS
Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

calc_centralize_matrixFunction to centralize a matrix X by column
calc_EGFunction to calculate the conditional expected genotype...
calc_EG_generalMore general function to calculate the conditional expected...
calc_EG_VarFunction to calculate the variance of conditional expected...
calc_EG_Var_generalFunction to calculate the variance of conditional expected...
calc_EMFunction to use EM algorithm to estimate the genotype...
calc_MrFunction to calcualte likelihood P(D|G) for simulating data,...
calc_pobs_ndepthFunction to calculate the likelihood matrix P(D|G) given a...
calc_psingleFunction to compute the genotype likelihood of a read given...
calc_robust_VarFunction to calcualte the robust variance of E(Gij|Dij) for...
calc_score_testFunction to calculate the score test for given expected...
calc_score_test1clac_score_test1 calculates the score test for given expected...
calc_ScoreVcalc_ScoreV gets score vector S for nsnp number of rare...
calc_ScoreV_likelycalc_ScoreV_likely: Get Variance of vector S by likelihood...
calc_ScoreV_regVarcalc_ScoreV_regVar: Get Variance of vector S by regular...
calc_ScoreV_RVScalc_ScoreV_RVS calculates variance of vector S by RVS using...
calc_simu_expFunction to calculate expected genotype data for simuation...
check_hom_matrixFunction to remove the homozygosity of a rare SNP in case or...
clistclist can combine two lists with the same structure.
combine_twogenoFunction to combine two sets of ped pairs for two samples
common_coordFunction to find the variants presenting in two datasets.
convertconvert two columns of a variant from ped file into additive...
cor.X.functionFunction to edit the correlation matrix of expected genotype...
filter_by_missFunction to filter out variants by missing rate p
filter_genocallFunction to filter out variants in the genotype hard call...
filter_VCF_SNPsFunction to filter variants in VCF files based on column 2...
generate_seq_1indGenerate sequence data for one indiviudal with read depth rd...
generate_seqdata_1varGenerate sequence data for ncase and ncontrol indiviudal at...
generate_seqdata_ORFunction to simulate data for one variant by given parameters
generate_seqdata_OR1Function to simulate data for one variant by given parameters
geno_add_2phenoFunction to add the phenotype in the 6th column of the...
geno_processFunction to deal with genotype hard call files in additive...
get_allele_frqFunction to calculate the allele frequency from additive...
get_exp_genoFunction to generates the expected probabilities of the...
get_exp_MAFFunction to calculate the minor allele frequency (MAF) from...
get_IDsFunction to seprates the case and control IDs.
get_likelihood_vcfFunction to get Likelihoods for all possible genotypes given...
get_lsingle_vcfFunction to parse Phred-scaled likelihoods
minor_alleleFunction to find the minor allele in the whole sample
odds.2.probsFunction to calculate the probability from given odds
ped_2_additiveFunction to combine two ped files for case and controls and...
rbindlistrbindlist can rbind combine two lists with the same...
regScore_permUse regular Score/Trend test for association for given...
regScore_RaoUse regular Score/Trend test for association for given...
regScore_rareIt calls functions...
regScore_rare1It calls functions...
reset_minor_additiveFunction to reset the additive coding genotype into nubmer of...
RVS_asyRVS using asymptotic distribution for score test statistic
RVS_btrapuse RVS to test associaton by bootrtrap, given phenotype (Y),...
RVS_rareIt calls functions...
RVS_rare1It calls functions...
RVS_rare2It calls functions...
sample_bootstrapFunction to bootstrap sampling
seq_callFunction to produce a sequencing read at one locus with...
seqdata_nvarGenerate sequence data for nsnp variants
seq_eg_frequse the simulated data to calculate the expected genotype...
sim.corr.binary.dataFunction to simulate the correlated binary data with given...
snp_true_2TFunction to change all TRUE genotype into T
subset_indFunction to take a subset the samples from a larger genotype...
subset_snpFunction to extract the genotype columns for chosen variants...
test_CalphaFunction to obtain p-value by Calpha method (quadratic test)...
test_CASTFunction to obtain p-value by CAST method (linear test) for J...
test_HotellingFunction to obtain pvalue by Hotelling test for J number of...
vcf_processthe main function to call the VCF file and return the...
Struglab/RVS documentation built on May 10, 2017, 3:34 p.m.